Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most of the differences in fruit size between Malus species. In this study, by using an interspecific hybrid population between Malus asiatica “Zisai Pearl” and Malus domestica cultivar “Red Fuji,” we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in Zisai Pearl led to a lower promoter activity than that of Red Fuji. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in Zisai Pearl, exerted significant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 confirmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malus accession and be potentially used in molecular assisted breeding via interspecific hybridization.

苹果品种的最终果实大小与果实生长过程中果皮细胞分裂和细胞扩张有关，但尚不清楚细胞分裂​​和/或细胞增大是否决定了苹果属物种之间果实大小的大部分差异。在本研究中，通过使用亚洲海棠“紫赛珍珠”和海棠品种“红富士”之间的种间杂交群体，我们发现中果皮细胞数量是海棠品种之间果实大小多样性的主要因素。中果皮细胞数量在花后28天（DAA）之前迅速增加，而细胞大小在28天DAA后逐渐增加直至果实成熟。通过结合 RNA-seq 数据和之前的果实重量 QTL 数据，预测了与生长素信号传导或细胞周期相关的 6 个候选基因。紫赛珍珠中生长素小RNA基因MdSAUR36启动子中的2个InDels和10个SNP导致其启动子活性低于红富士。紫赛珍珠杂合子MdSAUR36 ATG 密码子下游 379 bp 处的 1 个非同义 SNP G/T对果实重量、长度和宽度产生显着的基因型影响。通过过表达或RNAi MdSAUR36 的转基因苹果愈伤组织证实，MdSAUR36参与了中果皮细胞分裂和苹果果实大小的负调节。这些结果可以为苹果属品种小果实尺寸的分子机制提供新的见解，并有可能用于通过种间杂交进行分子辅助育种。